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### 4.3 MQTLView

MQTLView is designed to depict the result of the QTL clustering for one or several chromosomes on a given map.

#### 4.3.1 Command Line Options

Option | Usage | Type | Explanation
--- | --- | --- | ---
`-m,--map` | required | string | The XML file for the genetic map.
`-c,--chrom` | required | string | The name of the chromosome (or a list separated by comma) to display.
`-o,--output` | required | string | The output file stem.
`-r,--clust` | optional | string | The file of the clustering result.
`-b,--best` | optional | string | The file of the best clustering (only with -c).
`-t,--tree` | optional | string | The file of the hierarchical clustering result.
`--mode` | optional | integer | The mode of representation (0 or 1 and only with -c and -b)
`--trait` | optional | string | The name of the trait.
`-p,--parfile` | optional | string | The drawing parameter file.
`--img` | optional | string | The format of the image (use –help for possible values).

MQTLView provides several ways to represent the results of the QTL clustering depending on the algorithm used to perform it. Suppose we have first done a clustering using QTLClust See QTLClust, which produced the result file `clust_res.txt`. From the output file `clust_model.txt` generated by QTLClust we have derived the file `clust_best.txt` which gives for a given trait the best clustering model for each chromosome (according to a given model choice criterion):

         Chromosome      Trait   Model
         3       FT      5
         10      FT      4
         5       FT      4
         7       FT      5
         2       FT      4
         9       FT      2
         4       FT      3
         8       FT      5
         6       FT      3
         1       FT      2

Then, we can run MQTLView to visualize the result, for example on chromosome 8 and 9 together, by invoking the command

         %java org.metaqtl.main.MQTLView \
         >     -c 8,9 -m map.xml -r clust_res.txt -b clust_best.txt -o figure --img jpeg

By default the figure is created with the mode `--mode` 1 which leads to something like that

Now, if you set the option `--mode` to ```0``', i.e

         %java org.metaqtl.main.MQTLView \
         >     -c 8,9 -m map.xml -r clust_res.txt -b clust_best.txt -o figure --img jpeg --mode 0

you will obtain the following representation

where the first bar which follows the name of the QTL corresponds to the relative CI of the QTL (i.e. that the more the bar is filled, the larger the CI is). The second bar gives the membership probabilities of the QTL according to the meta-QTL model.

If the clustering have been done via QTLTree, the result file obtained `tree.txt` can be passed to MQTLView as follows,

         %java org.metaqtl.main.MQTLView \
         >     -c 3 -m map.xml -t tree.txt -o figure --img jpeg

In this case MQTLView draws the tree obtained by the hierarchical clustering procedure as illustrated in the next figure.

Finally the results from QTLClust and QTLTree can be visualized together as shown bellow.

         %java org.metaqtl.main.MQTLView \
         >     -c 3 -m map.xml -r clust_res.txt -b clust_best.txt -t tree.txt -o figure --img jpeg